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Eric Coissac
8c7017a99d
- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
35 lines
1.7 KiB
Markdown
35 lines
1.7 KiB
Markdown
# `obilua` Package: Biosequence Lua Bindings
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The `obilua` Go package provides **Lua bindings** for biological sequence objects (`obiseq.BioSequence`) used in the OBITools4 ecosystem. It enables scripting and automation of sequence analysis directly from Lua.
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## Core Functionality
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- **Type Registration**: Registers a new userdata type `BioSequence` in the Lua state, exposing methods and constructors.
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- **Constructor**:
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```lua
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BioSequence.new(id, sequence[, definition]) →BioSequence```
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- **Accessors & Mutators**:
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- `id()`, `sequence()`, `definition()` – get/set identifiers and sequence data.
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- `qualities([table])` – handle PHRED-quality scores (as Lua table or string).
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- `count()`, `taxid()` – numeric abundance and taxonomic ID.
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- **Taxonomy Integration**:
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- `taxon([Taxon])` – get/set taxonomic assignment via integrated taxonomy engine.
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- **Attributes**:
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- `attribute(name[, value])` – arbitrary metadata storage (supports tables, strings, numbers).
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- **Sequence Operations**:
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- `len()` – length of the sequence.
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- `has_sequence()`, `has_qualities()` – boolean checks for presence of data.
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- **Computation & Transformation**:
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- `subsequence(start, end)` – extract a region.
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- `reverse_complement()` → BioSequence.
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- `md5()`, `md5_string()` – compute sequence checksums (raw bytes or hex string).
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- **Serialization**:
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- `fasta([format])`, `fastq([format])` – output in FASTA/FASTQ, supporting `"json"` or `"obi"` header formats.
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- `string([format])` – smart formatting: FASTQ if qualities present, else FASTA.
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## Implementation Notes
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- Uses `gopher-lua` for interpreter integration.
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- UserData wrapping ensures type safety and GC management of Go-backed objects.
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- Error handling via Lua `ArgError` or `RaiseError`.
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